diff --git a/AUTHORS b/AUTHORS index 51b9aa8..f337646 100644 --- a/AUTHORS +++ b/AUTHORS @@ -60,16 +60,28 @@ ** ** Modifications to run under Microsoft Windows with Cygwin by: ** Sergio Daicz +** Gilles Detillieux ** -** Modifications to run on the Apple under Mac OS X +** Modifications to run on the Apple under Mac OS ** Alfonso Delgado-Reyes ** Josef Svitak +** Jan Pieczkowski +** Boris Marin +** +** Implementation of hsolvable STDP +** Dave Beeman +** Hugo Cornelis +** +** Addition of autoconf to automate Makefile construction +** Jan Pieczkowski +** Boris Marin ** ** Script Demos and Tutorials by: ** Dave Beeman ** Upinder S. Bhalla ** Sharon Crook ** Erik De Schutter +** Hugo Cornelis ** Mark E. Nelson ** Alex Protopapas ** Michael Vanier diff --git a/ChangeLog b/ChangeLog index 728dcd3..f3f86fa 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,7 +1,7 @@ G E N E S I S Summary of changes and revision history *************************************** - Last edited: $Date: Sat Oct 18 10:47:19 MDT 2014 $ + Last edited: $Date: Tue Nov 11 14:05:40 MST 2014 $ Each set of changes listed below is prefaced with the version number for which the changes apply. For development releases, two version numbers @@ -12,14 +12,16 @@ proposed release is subject to discussion and change. ------------------------------------------ FINAL RELEASE 2.4 -2014-October +2014-November ------------------------------------------ -- Three new network connection commands, 'volumeconnect3', -'volumeweight3', and 'volumedelay3', have been added and -documented. These allow distance-dependent connection -probabilities and/or weights and the use of periodic boundary -conditions for network connectivity. +- A new autoconf-based build system has been incorporated, so that a +simple "./configure" command will create the appropriate Makefile. + +- Three new network connection commands, 'volumeconnect3', 'volumeweight3', +and 'volumedelay3', have been added and documented. These allow +distance-dependent connection probabilities and/or weights and the use +of periodic boundary conditions for network connectivity. - Added HTML indexing to the 'genesis' directory and subdirectories. README files have been replaced or supplemented with '.txt' or '.html' files. diff --git a/ChangeLog.txt b/ChangeLog.txt index 728dcd3..f3f86fa 100644 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,7 +1,7 @@ G E N E S I S Summary of changes and revision history *************************************** - Last edited: $Date: Sat Oct 18 10:47:19 MDT 2014 $ + Last edited: $Date: Tue Nov 11 14:05:40 MST 2014 $ Each set of changes listed below is prefaced with the version number for which the changes apply. For development releases, two version numbers @@ -12,14 +12,16 @@ proposed release is subject to discussion and change. ------------------------------------------ FINAL RELEASE 2.4 -2014-October +2014-November ------------------------------------------ -- Three new network connection commands, 'volumeconnect3', -'volumeweight3', and 'volumedelay3', have been added and -documented. These allow distance-dependent connection -probabilities and/or weights and the use of periodic boundary -conditions for network connectivity. +- A new autoconf-based build system has been incorporated, so that a +simple "./configure" command will create the appropriate Makefile. + +- Three new network connection commands, 'volumeconnect3', 'volumeweight3', +and 'volumedelay3', have been added and documented. These allow +distance-dependent connection probabilities and/or weights and the use +of periodic boundary conditions for network connectivity. - Added HTML indexing to the 'genesis' directory and subdirectories. README files have been replaced or supplemented with '.txt' or '.html' files. diff --git a/README b/README index 2d16b5b..c0bc2a0 100644 --- a/README +++ b/README @@ -1,11 +1,10 @@ :: - G E N E S I S - + G E N E S I S The GEneral NEural Simulation System - Version 2.4 - Last edited: $Date:Fri Oct 17 15:49:46 MDT 2014 $ + Version 2.4 + Last edited: $Date: Tue Nov 11 13:00:14 MST 2014 $ Introduction ------------ @@ -53,9 +52,10 @@ Obtaining GENESIS ------------------ GENESIS source and binary distributions can be obtained from: -http://sourceforge.net/projects/genesis-sim, and http://genesis-sim.org. +http://genesis-sim.org, or from the Sourceforge GENESIS 2 development +site http://sourceforge.net/projects/genesis-sim. -Machine dependence +Machine dependence ------------------ GENESIS and its graphical front-end XODUS are written in C and are @@ -64,7 +64,11 @@ known to run under many UNIX-based systems with the X Window System recent experiences are with Fedora and Ubuntu. It has also been used under various MS Windows virtual environments for running Linux. -Here is a partial list of tested older platforms: +The current GENESIS 2.4 version has been tested on various recent Linux +distributions including Debian, Ubuntu, and Fedora, on Mac OSX (intel), +and Cygwin (32 bit version, which works with 64 bit Windows). + +Here is a partial list of older platforms tested for version 2.3: * x86-based Linux systems: + Debian Linux with kernel 2.x @@ -74,7 +78,7 @@ Here is a partial list of tested older platforms: + Red Hat Linux 5, 6, 7, 8, and 9 + Slackware 10 * 64 bit Linuces: - + Fedora Core 3 and 4 + + Fedora Core 3 and 4, Fedora 10 - 19. + Red Hat Enterprise * x86-based FreeBSD 4.1 * Alpha with Debian 3.0 diff --git a/README.bindist b/README.bindist index 24737aa..91c9b8f 100644 --- a/README.bindist +++ b/README.bindist @@ -7,7 +7,9 @@ the form of 'genesis-2.4--bin.tar.gz' files. Binary distributions of GENESIS 2.4 for Debian (.deb) and Fedora (.rpm) Linux should be available from the GENESIS web site shortly -after the November 1014 GENESIS 2.4 release. +after the November 2014 GENESIS 2.4 release. Distributions for Mac OS +and Cygwin should follow. Look for updated installation instructions +in the genesis-2.4/genesis directory of the binary distribution. CONTENTS 1 QUICK START @@ -51,7 +53,7 @@ The genesis executables have been linked with certain versions of dynamic libraries. These libraries must be available at run time. See the Operating System Specific Notes below. If have problems running this distribution or want to compile your own version of GENESIS, please get the source distribution -from http://sourceforge.net/projects/genesis-sim. +from http://genesis-sim.org/GENESIS or http://sourceforge.net/projects/genesis-sim. 3 INSTALLATION @@ -68,7 +70,7 @@ example, cd /usr/local tar xvzf /mnt/cdrom/genesis-2.4-linux-bin.tar.gz -or from wherever you have it (e.g.~/downloads/genesis-2.3-linux-bin.tar.gz) +or from wherever you have it (e.g.~/downloads/genesis-2.r-linux-bin.tar.gz) 3.2 Site-specific Setup @@ -138,19 +140,32 @@ installed operating system. So, the GENESIS executables have been linked against dynamic libraries creating runtime dependencies as described below. - 4.1 Cygwin Cygwin provides a UNIX-like environment for Windows that will let you run GENESIS and other UNIX programs that have been compiled to run under Cygwin. -Go to http://cygwin.com, and look for the "Install Cygwin now" link. This -will download a small setup.exe, which will let you choose what to install and -then download it. For more information about selecting packages to install, -use the link for "Help on setup.exe". For more information on Cygwin, see -the Cygwin users guide at http://cygwin.com/cygwin-ug-net/ -More information on installing and using X windows with Cygwin can be found in -the Cygwin/X User's Guide at http://x.cygwin.com/docs/ug/cygwin-x-ug.html +Go to http://cygwin.com, and install it by downloading and running +setup-x86.exe (32-bit installation). This may be used with 64 bit MS Windows, +and is recommended over the less stable setup-x86_64.exe. + +Running this will let you choose what to install and +then download it. + +When using Cygwin Setup for the first time, the default is to install +a minimal subset of all available packages. If you want anything +beyond that, you will have to select it explicitly. See +http://cygwin.com/packages/ for a searchable list of available +packages, or use cygcheck -p as described in the Cygwin User's Guide +at http://cygwin.com/cygwin-ug-net/using-utils.html#cygcheck. + +To build GENESIS, you will need gcc, binutils, make and probably other +packages from the ``Devel'' category. Text editors can be found under +``Editors''. For more information about selecting packages to install, +and using Cygwin, consult the docmentation links at http://cygwin.com. + +More information on installing and using X windows with Cygwin can be found +at http://x.cygwin.com/. GENESIS can be run under Windows with the Cygwin software installed. If you want to run GENESIS with GUI capabilities, the X windows package must be installed @@ -206,30 +221,31 @@ Graphical GENESIS (genesis) needs these additional libraries: libX11.so.6 libdl.so.2 - and possibly: + and possibly (but unlikely): libSM.so.6 libICE.so.6 Given the variety of Linuces available each with it's own package management system, there's no standard process for installing these libraries. Try to -get packages from your OS vendor's web site. You'll need libc6 and X11R6. +get packages from your OS vendor's web site. You'll need libc6 and X.org. 4.3 OSX Darwin The OSX executables were built using Xcode 2.2 tools, based on GCC 4.0. -The binary distribution of GENESIS will only work with OSX 10.2 and higher, -on the PowerPC architectures. You'll have to compile the package -from source to run on earlier versions or on the Intel architecture. +The binary distribution of GENESIS will only work with OSX 10.8 and higher, +on intel architectures. You'll have to compile the package +from source to run on earlier versions or on the PPC architecture. -The non-graphical version of GENESIS (nxgenesis) should run on any standard -OSX installation. Graphical GENESIS (genesis) relies on the X11 libraries for -it's graphical user interface (GUI). An X11 server needs to be started before -graphical GENESIS can be run. If you can't locate the X11 application (usually -Applications->Utilities->X11), see: -http://developer.apple.com/darwin/runningX11.html -for further information. +The non-graphical version of GENESIS (nxgenesis) should run on any +standard OSX installation. Graphical GENESIS (genesis) relies on the +X11 libraries for it's graphical user interface (GUI). An X11 server +needs to be started before graphical GENESIS can be run. If you can't +locate the X11 application (perhaps in Applications->Utilities->X11), +see: https://developer.apple.com/opensource/ or the XQuartz project +(http://xquartz.macosforge.org/landing/). See src/README.OSX for more +details. Starting the X11 application should bring up an 'xterm' window. Graphical GENESIS must be started from the xterm window; it will not work from a window @@ -238,7 +254,7 @@ started by the 'Terminal' application. 5 PROBLEMS RUNNING GENESIS -You must be running X11R5 or X11R6 in order to successfully run the +You must be running X.org, X11R5 or X11R6 in order to successfully run the graphical GENESIS. Earlier versions will not work. SGI users: if your X11 server is set up to default to a diff --git a/README.html b/README.html index 7e94719..5bdcaba 100644 --- a/README.html +++ b/README.html @@ -5,6 +5,7 @@ +
@@ -17,11 +18,10 @@ 

-                    G E N E S I S
-
+                G E N E S I S
         The GEneral NEural Simulation System
-                       Version 2.4
-Last edited: $Date: Fri Oct 17 15:49:46 MDT 2014 $
+                   Version 2.4
+Last edited: $Date: Tue Nov 11 13:00:14 MST 2014 $

Introduction

@@ -31,25 +31,13 @@

Introduction

ChangeLog.txt. New features of version 2.3 and 2.4 are described in Doc/Changes.txt.

- -

Directions for installing binary distributions may be found in -README.bindist in this directory. Directions for building and -installing source distributions are -in src/README.html. Be sure to read the -directions concerning the installation of the ".simrc" -file.

- -

The HTML documentation for GENESIS is in -Hyperdoc/Manual.html and its links. -Directions for printing and using the plan text documentation may be found in -Doc/README.txt. -The Scripts/README.html file describes -the demonstration and tutorial simulations which are included with -this distribution.

For additional tutorials and simulation -scripts, see the "Ultimate GENESIS Tutorial Distribution" at - -http://genesis-sim.org/GENESIS/UGTD.html. - +

Directions for installing binary distributions may be found in README.bindist +in this directory. Directions for building and installing source distributions +are in src/README. Be sure to read the directions +concerning the installation of the ".simrc" file. Directions for printing +and using the documentation may be found in Doc/README. The +Scripts/README file describes the demonstration and tutorial simulations +which are included with this distribution.

Description of GENESIS

@@ -68,16 +56,15 @@

Description of GENESIS

Beeman, Springer-Verlag (1998). The free Internet Edition is available at http://www.genesis-sim.org/GENESIS/bog/bog.html

Additional hypertext documentation, including a beginners guide to -UNIX/Linux commands, can be found in genesis/Tutorials.

+UNIX/Linux commands, can be found in genesis/Tutorials.

Source code contributed by GENESIS users which must be compiled is found in -src/contrib; other contributions, such as scripts and utilities are in -contrib.

- +src/contrib; other contributions, such as scripts and utilities are in contrib.

Obtaining GENESIS

GENESIS source and binary distributions can be obtained from: -http://sourceforge.net/projects/genesis-sim, and http://genesis-sim.org.

+http://genesis-sim.org, or from the Sourceforge GENESIS 2 development +site http://sourceforge.net/projects/genesis-sim.

Machine dependence

@@ -86,7 +73,10 @@

Machine dependence

(X11R5, X11R6, Xorg), as well as OSX and Windows with Cygwin. Most recent experiences are with Fedora and Ubuntu. It has also been used under various MS Windows virtual environments for running Linux.

-

Here is a partial list of tested older platforms:

+

The current GENESIS 2.4 version has been tested on various recent Linux +distributions including Debian, Ubuntu, and Fedora, on Mac OSX (intel), +and Cygwin (32 bit version, which works with 64 bit Windows).

+

Here is a partial list of older platforms tested for version 2.3:

  • x86-based Linux systems:
    @@ -104,7 +94,7 @@

    Machine dependence

  • 64 bit Linuces:
      -
    • Fedora Core 3 and 4
      • +
    • Fedora Core 3 and 4, Fedora 10 - 19.
    • Red Hat Enterprise
    @@ -190,12 +180,10 @@

    Copyright Notice

-

Return to the GENESIS main index

-